Statistical theory of any physical process needs a formulation of possibly simple but adequate models of the phenomena underlying microscopic dynamics. Remarkable progress in studies of internal dynamics of biomolecules acomplished in the recent years has made it possible to formulate such...

Identification of proton-conducting pathways in a protein is a key to understanding the mechanisms of biomolecular proton transfer. Starting from a known protein structure, proton pathways are modeled here as hydrogen bonded networks of proton conducting groups, including proton-exchanging...

Molecular dynamics simulations of plastocyanin, an electron transfer copper containing protein involved in the photosynthetic process, have been performed in both the hydrated and dry state. An analysis of the potential energy fluctuations during a 500 ps dynamical evolution of the macromolecule...

A realistic physical model for the so-called rate-promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so-called discrete breather...

Protein activities may exhibit oscillations which often occur due to the existence of a negative feedback loop with an effective time delay. Many biological systems are, however, not limited to one feedback loop but consist of multiple loops on different regulatory levels. Here, we analyze the...

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion process (ASEP). The model is formulated to account for (i) excluded-volume interactions, (ii) the observed asymmetry of the stochastic movement of individual...

Helicases are one of the smallest motors of biological system, which harness the chemical free energy of ATP hydrolysis to catalyze the opening of energetically stable duplex nucleic acids and thereby are involved in almost all aspect of nucleic acid metabolism including replication, repair,...

Can the different causes for disruption of intracellular transport be traced from the trajectories of the molecular motors on the cytoskeletal filaments? We will attempt to answer this important question in a Monte Carlo model of microtubule–motor protein interaction from the point of view of...

Molecular motors are single macromolecules that generate forces at the piconewton range and nanometer scale. They convert chemical energy into mechanical work by moving along filamentous structures. In this paper, we study the velocity of two-head molecular motors in the framework of a...